Last updated: 2019-03-01
Checks: 4 2
Knit directory: DNASeq/
This reproducible R Markdown analysis was created with workflowr (version 1.2.0). The Report tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
The R Markdown is untracked by Git. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.
wflow_publish or wflow_build to ensure that the code is always run in an empty environment. The following objects were defined in the global environment when these results were created:
| Name | Class | Size |
|---|---|---|
| a | packageIQR | 2.3 Kb |
| alignMerge | cwlStepParam | 306.3 Kb |
| bwa | cwlParam | 25.2 Kb |
| bwaAlign | cwlStepParam | 125.7 Kb |
| dats | packageIQR | 2.3 Kb |
| f1 | InputParam | 2.8 Kb |
| f2 | InputParam | 2.8 Kb |
| f3 | InputParam | 2.8 Kb |
| fastqc | cwlParam | 13.8 Kb |
| featureCounts | cwlParam | 19.4 Kb |
| fq1 | list | 832 bytes |
| fq2 | list | 832 bytes |
| fq2ubamJson | cwlParam | 37.4 Kb |
| GAlign | cwlStepParam | 211.9 Kb |
| geneBody_coverage | cwlParam | 21.8 Kb |
| genePredToBed | cwlParam | 16.5 Kb |
| gtfToGenePred | cwlParam | 16.5 Kb |
| hapCall | cwlStepParam | 29.6 Kb |
| hapJson | cwlParam | 19.3 Kb |
| inputList | list | 3.5 Kb |
| jdCall | cwlStepParam | 129.5 Kb |
| jdJson | cwlParam | 28.3 Kb |
| markdup | cwlParam | 21.8 Kb |
| mc3 | cwlStepParam | 90.6 Kb |
| mergeBam | cwlParam | 18.4 Kb |
| mergeBamDup | cwlStepParam | 122.7 Kb |
| mvOut | cwlParam | 13.4 Kb |
| o1 | OutputParam | 2.3 Kb |
| o2 | OutputParam | 2.3 Kb |
| o2a | OutputParam | 2.3 Kb |
| o2b | OutputParam | 2.3 Kb |
| o2c | OutputParam | 2.3 Kb |
| o3 | OutputParam | 2.3 Kb |
| o4 | OutputParam | 2.4 Kb |
| o5 | OutputParam | 2.4 Kb |
| o6 | OutputParam | 2.4 Kb |
| o7 | OutputParam | 2.3 Kb |
| o8 | OutputParam | 2.3 Kb |
| p1 | InputParam | 2.8 Kb |
| p10 | InputParam | 2.8 Kb |
| p11 | InputParam | 2.8 Kb |
| p12 | InputParam | 2.8 Kb |
| p13 | InputParam | 2.8 Kb |
| p2 | InputParam | 2.8 Kb |
| p3 | InputParam | 2.8 Kb |
| p4 | InputParam | 2.8 Kb |
| p5 | InputParam | 2.8 Kb |
| p6 | InputParam | 2.8 Kb |
| p7 | InputParam | 2.8 Kb |
| p8 | InputParam | 2.8 Kb |
| p9 | InputParam | 2.8 Kb |
| paramList | list | 576 bytes |
| read_distribution | cwlParam | 16.6 Kb |
| req1 | list | 416 bytes |
| req2 | list | 416 bytes |
| req3 | list | 416 bytes |
| rgs | list | 880 bytes |
| rnaseq_Sf | cwlStepParam | 315.6 Kb |
| rscripts | character | 816 bytes |
| RSeQC | cwlStepParam | 126 Kb |
| runWDL | cwlParam | 21.7 Kb |
| s1 | stepParam | 19.5 Kb |
| s2 | stepParam | 44.2 Kb |
| s3 | stepParam | 20.1 Kb |
| s4 | stepParam | 19.5 Kb |
| s5 | stepParam | 28.1 Kb |
| s6 | stepParam | 133.4 Kb |
| sam2bam | cwlParam | 13.9 Kb |
| samples | list | 592 bytes |
| samtools_flagstat | cwlParam | 13.8 Kb |
| samtools_index | cwlParam | 14.4 Kb |
| sortBam | cwlParam | 13.8 Kb |
| STAR | cwlParam | 32.2 Kb |
| ubam2bamJson | cwlParam | 16.6 Kb |
The command set.seed(20181205) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Untracked files:
Untracked: analysis/Rcwl_DNASeq_Align.Rmd
Untracked: analysis/Rcwl_DNASeq_Align.Rmd~
Untracked: analysis/Rcwl_GATK4.Rmd
Untracked: analysis/Rcwl_GATK4.Rmd~
Untracked: analysis/Rcwl_MC3.Rmd
Untracked: analysis/Rcwl_MC3.Rmd~
Untracked: bwaOutput.sam
Untracked: code/gatk.R
Untracked: code/gatk.R~
Untracked: data/fq1_1.fq
Untracked: data/fq1_2.fq
Untracked: data/fq2_1.fq
Untracked: data/fq2_2.fq
Untracked: data/normal.bam
Untracked: data/normal.bam.bai
Untracked: data/normal_1.fq
Untracked: data/normal_2.fq
Untracked: data/tumor.bam
Untracked: data/tumor.bam.bai
Untracked: data/tumor_1.fq
Untracked: data/tumor_2.fq
Untracked: file3f79542e1d70/
Untracked: output/BAM/
Untracked: output/GATK/
Untracked: output/interval.21.interval_list
Untracked: output/interval.21.intervals
Untracked: output/interval.list~
Untracked: output/interval.txt
Untracked: output/mc3/
Untracked: sample1.bam
Untracked: sample1.bam.bai
Untracked: temp/DNASeq.Rmd
Untracked: temp/DNASeq.Rmd~
Untracked: temp/analysis/filed13439812939/
Untracked: temp/analysis/temp/
Untracked: temp/data/test.1_fastq.gz
Untracked: temp/data/test.2_fastq.gz
Untracked: temp/output/BAM/
Untracked: test.bam
Untracked: tmpl1.json
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
There are no past versions. Publish this analysis with wflow_publish() to start tracking its development.
The Multi-Center Mutation Calling in Multiple Cancers project (MC3) pipeline was developed by TCGA to generate a comprehensive encyclopedia of somatic mutation calls by applying an ensemble of seven mutation-calling algorithms with scoring and artifact filtering. More details can be found in this paper: Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines
The mc3 pipeline is available at https://github.com/OpenGenomics/mc3. All required software have been deployed in cloud with docker.
The pipeline has been imported and contained in the RcwlPipelines pacakge, which contains two major steps (markID step was removed):
Here is the short summary.
suppressPackageStartupMessages(library(Rcwl))
library(RcwlPipelines)
data(mc3)
short(mc3)
inputs:
- tumorID
- normalID
- tumor
- normal
- bed_file
- centromere
- cosmic
- dbsnp
- refFasta
- vepData
outputs:
- outmaf
- outvcf
steps:
- call_variants
- convert
plotCWL(mc3)
callVar <- readCWL(runs(mc3)$call_variants)
plotCWL(callVar)
conv <- readCWL(runs(mc3)$convert)
plotCWL(conv)
Testing somatic mutation data can be download from: https://github.com/genome/somatic-snv-test-data.
inputList. The tumorID/normalID must be consistent with SM from BAM read group.inputList <- list(tumorID=list(test="NA12892"),
normalID=list(test="NA12878"),
tumor=list(test="data/tumor.bam"),
normal=list(test="data/normal.bam"))
paramList.paramList <- list(bed_file="/mnt/lustre/users/qhu/software/mc3/data/gaf_20111020+broad_wex_1.1_hg19.bed",
centromere="/mnt/lustre/users/qhu/software/mc3/data/centromere_hg19.bed",
cosmic="/mnt/lustre/users/qhu/software/mc3/data/hg19_cosmic_v54_120711.vcf.gz",
dbsnp="/mnt/lustre/users/qhu/software/mc3/data/dbsnp_134_b37.leftAligned.vcf.gz",
refFasta="/rpcc/bioinformatics/reference/current/human_g1k_v37.fa.gz",
vepData="/home/qhu/.vep/")
res <- runCWLBatch(mc3, outdir = "output/mc3",
inputList = inputList, paramList = paramList,
BPPARAM = BatchtoolsParam(workers = 1, cluster = "sge",
template = "/rpcc/bioinformatics/sge_centos7.tmpl",
resources = list(threads = 2,
queue = "centos7.q")))
The final VCF was filtered and merged from the outputs of different pipelines and annotated by VEP. The converted MAF file was also generated.
dir("output/mc3/test")
[1] "merged.vep.vcf" "vep.maf"
vcf <- read.table("output/mc3/test/merged.vep.vcf", sep="\t")
head(vcf)
V1 V2 V3 V4 V5 V6 V7
1 21 10400299 . A T 0.0 PASS
2 21 10400380 . C T . PASS
3 21 10402435 rs2948877 G A . PASS
4 21 10402715 . G A 0.0 PASS
5 21 10402795 rs148043841 G T . PASS
6 21 10402985 . G GA . PASS
V8
1 CENTERS=RADIA|VARSCANS|MUSE|SOMATICSNIPER;CSQ=T|intergenic_variant|MODIFIER|||||||||||||||rs370695467|1||||1|SNV|1|||||||||||||||||||||||||||||||
2 CENTERS=SOMATICSNIPER|RADIA|VARSCANS|MUSE;CSQ=T|intergenic_variant|MODIFIER||||||||||||||||1||||1|SNV|1|||||||||||||||||||||||||||||||
3 CENTERS=MUSE|RADIA|VARSCANS|SOMATICSNIPER;CSQ=A|intergenic_variant|MODIFIER|||||||||||||||rs2948877|1||||1|SNV|1||||||||||||||||A:0.3626|A:0.4266|A:0.3228|A:0.3075|A:0.2913|A:0.4346||||||||||
4 CENTERS=RADIA|VARSCANS|MUSE;CSQ=A|intergenic_variant|MODIFIER|||||||||||||||rs2948878|1||||1|SNV|1|||||||||||||||||||||||||||||||
5 CENTERS=MUSE|RADIA|VARSCANS;CSQ=T|intergenic_variant|MODIFIER|||||||||||||||rs373568457|1||||1|SNV|1|||||||||||||||||||||||||||||||
6 CENTERS=VARSCANI*|PINDEL;CSQ=A|intergenic_variant|MODIFIER|||||||||||||||rs375209288|1||||1|insertion|1|||||||||||||||||||||||||||||||
V9 V10 V11
1 GT:DP:AD 0/0:140:140,0 0/1:92:71,20
2 GT:DP:AD 0/0:160:160,0 0/1:117:99,18
3 GT:DP:AD 0/0:167:167,0 0/1:124:97,27
4 GT:DP:AD 0/0:145:145,0 0/1:117:97,20
5 GT:DP:AD 0/0:163:161,2 0/1:127:108,19
6 GT:DP:AD 0/0:88:88,0 0/1:82:75,7
sessionInfo()
R version 3.5.2 Patched (2018-12-31 r75935)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.4 (Final)
Matrix products: default
BLAS: /home/qhu/usr/R-3.5/lib64/R/lib/libRblas.so
LAPACK: /home/qhu/usr/R-3.5/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] RcwlPipelines_0.99.0 testthat_2.0.1 BiocStyle_2.10.0
[4] rmarkdown_1.11 knitr_1.21 usethis_1.4.0
[7] devtools_2.0.1 Rcwl_0.99.14 S4Vectors_0.20.1
[10] BiocGenerics_0.28.0 yaml_2.2.0
loaded via a namespace (and not attached):
[1] colorspace_1.4-0 rprojroot_1.3-2 fs_1.2.6
[4] rstudioapi_0.9.0 roxygen2_6.1.1 remotes_2.0.2
[7] xml2_1.2.0 pkgload_1.0.2 jsonlite_1.6
[10] workflowr_1.2.0 shiny_1.2.0 DiagrammeR_1.0.0
[13] BiocManager_1.30.4 readr_1.3.1 compiler_3.5.2
[16] backports_1.1.3 assertthat_0.2.0 lazyeval_0.2.1
[19] cli_1.0.1 later_0.8.0 visNetwork_2.0.5
[22] htmltools_0.3.6 prettyunits_1.0.2 tools_3.5.2
[25] igraph_1.2.4 gtable_0.2.0 glue_1.3.0
[28] dplyr_0.8.0.1 batchtools_0.9.11 rappdirs_0.3.1
[31] Rcpp_1.0.0 rgexf_0.15.3 xopen_1.0.0
[34] debugme_1.1.0 xfun_0.5 stringr_1.4.0
[37] ps_1.3.0 mime_0.6 XML_3.98-1.17
[40] scales_1.0.0 hms_0.4.2 promises_1.0.1
[43] RColorBrewer_1.1-2 memoise_1.1.0 gridExtra_2.3
[46] ggplot2_3.1.0 downloader_0.4 rcmdcheck_1.3.2
[49] stringi_1.3.1 highr_0.7 Rook_1.1-1
[52] desc_1.2.0 checkmate_1.9.1 pkgbuild_1.0.2
[55] BiocParallel_1.16.6 rlang_0.3.1 pkgconfig_2.0.2
[58] commonmark_1.7 evaluate_0.13 purrr_0.3.0
[61] htmlwidgets_1.3 processx_3.2.1 tidyselect_0.2.5
[64] plyr_1.8.4 magrittr_1.5 bookdown_0.9
[67] R6_2.4.0 base64url_1.4 pillar_1.3.1
[70] withr_2.1.2 tibble_2.0.1 crayon_1.3.4
[73] viridis_0.5.1 progress_1.2.0 grid_3.5.2
[76] data.table_1.12.0 git2r_0.24.0 callr_3.1.1
[79] influenceR_0.1.0 digest_0.6.18 xtable_1.8-3
[82] tidyr_0.8.2 httpuv_1.4.5.1 brew_1.0-6
[85] munsell_0.5.0 viridisLite_0.3.0 sessioninfo_1.1.1